Markers + reference

Gymnospermium

8 species · Berberidaceae · Ranunculales

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Species 8
Genome length 158–161 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 863 0.0356 0.83 68.5 yes View details
trnK-UUU-rps16 LSC 808 0.0201 0.98 60.3 yes View details
trnT-GGU-psbD LSC 1670 0.0147 0.97 61.7 yes View details
psbZ-trnG-UCC LSC 512 0.0438 0.96 74.6 yes View details
trnT-UGU-trnL-UAA LSC 601 0.0426 1.00 78.5 yes View details
rpl33-rps18 LSC 315 0.1006 0.97 74.0 yes View details
ndhF SSC 2151 0.0073 1.00 44.1 yes View details
ndhF-rpl32 SSC 1190 0.0224 0.95 69.4 yes View details
ccsA-ndhD SSC 301 0.0520 0.98 74.0 yes View details
ndhG-ndhI SSC 510 0.0303 0.94 67.9 yes View details
psbC-trnS-UGA LSC 172 0.0385 1.00 80.4 yes View details
rps19 IRa 173 0.0581 1.00 71.2 no View details
rpl14-rpl16 LSC 124 0.0564 1.00 69.9 yes View details
ycf1-ndhF SSC 159 0.2528 0.92 69.4 yes View details
trnR-UCU-atpA LSC 124 0.0383 1.00 65.9 yes View details
psbI-trnS-GCU LSC 147 0.0256 1.00 62.9 yes View details
psbM-trnD-GUC LSC 1232 0.0088 0.99 61.7 yes View details
atpH-atpI LSC 1155 0.0079 1.00 61.0 yes View details
trnC-GCA-petN LSC 906 0.0082 0.99 58.1 yes View details
ycf3-trnS-GGA LSC 925 0.0135 1.00 57.7 yes View details
rps19 IRb 279 0.0047 1.00 27.4 no View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT AAGCTCCATCTACGAATGGC 790–914 1.000 88.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC AAGCTCCATCTACGAATGGC 791–915 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG AAGCTCCATCTACGAATGGC 783–907 1.000 86.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT AGCTCCATCTACGAATGGCT 789–913 1.000 85.8
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC AAGCTCCATCTACGAATGGC 812–936 1.000 85.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAAGGCGCTCAACCTACA 1003–1222 1.000 85.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1002–1221 1.000 85.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAGGGGGTTAGAGACAGCT 1438–1687 1.000 85.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGGGGGTTAGAGACAGCT 1437–1686 1.000 85.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTGCGGCTCTATCCATTT AAAAAGGCGCTCAACCTACA 1158–1377 1.000 85.3
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TAAAGCGGCGGATTGCTAAT 249–275 1.000 82.9
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TTTTTCGTACCGAGGGTTCG 217–243 1.000 82.2
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT ATTGGGAGAGATGGCTGAGT 273–299 1.000 81.9
psbI-trnS-GCU_p4 psbI-trnS-GCU AATGATCCAGGGCGTAATCC TAAAGCGGCGGATTGCTAAT 250–276 1.000 80.4
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT ATGGCTGAGTGGTCTAAAGC 263–289 1.000 79.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCGAAGAGGCAGAAGTACT 224–226 1.000 71.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGACCGAAGAGGCAGAAGTA 226–228 1.000 71.5
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTGACCGAAGAGGCAGAA 229–231 1.000 71.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTGACCGAAGAGGC 233–235 1.000 71.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GACCGAAGAGGCAGAAGTAC 225–227 1.000 69.9
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATAGGGGAATCCATGGAGGG 1072–1354 1.000 85.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1029–1311 1.000 85.0
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1085–1367 1.000 84.3
atpH-atpI_p4 atpH-atpI CAATAGAAGCCAGCCCTACG ATAGGGGAATCCATGGAGGG 1064–1346 1.000 84.2
atpH-atpI_p5 atpH-atpI GATACCTTCTACGGCTTGGC ATAGGGGAATCCATGGAGGG 1114–1396 1.000 84.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 964–1002 1.000 84.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 958–996 1.000 83.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 982–1020 1.000 82.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1018–1056 1.000 81.9
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 976–1014 1.000 81.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Gymnospermium albertii NC_065737.1 157959 View on NCBI ↗
Gymnospermium altaicum NC_065738.1 158076 View on NCBI ↗
Gymnospermium darwasicum NC_065739.1 158584 View on NCBI ↗
Gymnospermium microrrhynchum NC_030061.1 160533 View on NCBI ↗
Gymnospermium odessanum NC_065740.1 158234 View on NCBI ↗
Gymnospermium peloponnesiacum NC_065741.1 158253 View on NCBI ↗
Gymnospermium scipetarum NC_065742.1 157818 View on NCBI ↗
Gymnospermium vitellinum NC_065744.1 158563 View on NCBI ↗